Contacts of the strand formed by residues 8 - 12 (chain O) in PDB entry 4C4K
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 8 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7O SER* 1.4 75.6 + - - +
9O ALA* 1.4 62.6 + - - +
35O GLY* 4.1 3.8 - - - -
36O ASN* 2.7 53.3 + - - +
86O ASN* 3.0 11.9 + - - -
88O ILE* 3.9 6.8 - - - +
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Residues in contact with ALA 9 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O SER* 1.4 78.0 + - - +
10O PRO* 1.4 78.8 - - + +
11O ARG* 3.7 4.9 + - - +
34O VAL 4.2 1.9 - - - +
35O GLY* 4.4 2.0 - - - -
88O ILE* 3.8 15.1 - - + +
89O GLY* 4.5 1.6 - - - +
90O GLU 6.1 0.2 - - - +
21T VAL* 3.6 43.1 - - + +
23T THR* 5.4 1.1 - - + -
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Residues in contact with PRO 10 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O ALA* 1.4 86.5 - - + +
11O ARG* 1.3 59.8 + - - +
33O ILE* 4.5 0.7 - - + -
34O VAL 3.2 11.7 - - - +
35O GLY* 4.2 1.8 - - - -
39O PRO* 4.0 15.9 - - + -
84O ALA* 3.7 33.2 - - + +
86O ASN* 3.4 19.7 - - - +
89O GLY 3.3 33.4 - - - +
90O GLU* 4.0 1.7 - - - +
91O ALA* 3.7 6.5 + - + +
23T THR* 3.6 24.3 + - - +
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Residues in contact with ARG 11 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O ALA 4.5 4.0 - - - +
10O PRO* 1.3 75.3 - - - +
12O PHE* 1.3 79.1 + - - +
13O LEU* 3.5 19.8 + - - +
33O ILE* 3.4 6.0 - - - +
34O VAL* 2.8 42.1 + - + +
91O ALA* 4.6 2.5 - - - -
23T THR* 4.9 4.5 - - + -
56T GLU* 3.0 42.7 + - - -
63T THR* 5.3 8.0 + - + +
65T ILE* 4.8 9.1 - - - +
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Residues in contact with PHE 12 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11O ARG* 1.3 81.1 + - - +
13O LEU* 1.3 64.7 + - - +
14O THR 3.9 12.3 - - - +
16O PRO* 5.0 2.2 - - + -
31O CYS* 3.6 35.0 - - + -
32O GLN 3.4 4.0 - - - -
33O ILE* 3.7 21.5 - - + +
82O CYS* 3.6 29.6 - - + -
83O ARG 4.9 0.2 - - - -
84O ALA* 4.9 1.8 - - + -
91O ALA* 3.6 27.4 - - + -
92O PHE 3.6 23.8 - - - -
93O ALA* 3.6 22.4 - - + -
23T THR* 5.2 2.2 + - - -
25T ALA* 4.4 16.6 - - + -
61T LEU* 4.5 10.5 - - + +
63T THR* 5.5 1.4 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il